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Khan I, Li S, Tao L, Wang C, Ye B, Li H, Liu X, Ahmad I, Su W, Zhong G, Wen Z, Wang J, Hua RH, Ma A, Liang J, Wan XP, Bu ZG, Zheng YH. Tubeimosides are pan-coronavirus and filovirus inhibitors that can block their fusion protein binding to Niemann-Pick C1. Nat Commun 2024; 15:162. [PMID: 38167417 PMCID: PMC10762260 DOI: 10.1038/s41467-023-44504-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
SARS-CoV-2 and filovirus enter cells via the cell surface angiotensin-converting enzyme 2 (ACE2) or the late-endosome Niemann-Pick C1 (NPC1) as a receptor. Here, we screened 974 natural compounds and identified Tubeimosides I, II, and III as pan-coronavirus and filovirus entry inhibitors that target NPC1. Using in-silico, biochemical, and genomic approaches, we provide evidence that NPC1 also binds SARS-CoV-2 spike (S) protein on the receptor-binding domain (RBD), which is blocked by Tubeimosides. Importantly, NPC1 strongly promotes productive SARS-CoV-2 entry, which we propose is due to its influence on fusion in late endosomes. The Tubeimosides' antiviral activity and NPC1 function are further confirmed by infection with SARS-CoV-2 variants of concern (VOC), SARS-CoV, and MERS-CoV. Thus, NPC1 is a critical entry co-factor for highly pathogenic human coronaviruses (HCoVs) in the late endosomes, and Tubeimosides hold promise as a new countermeasure for these HCoVs and filoviruses.
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Affiliation(s)
- Ilyas Khan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Sunan Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lihong Tao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chong Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Bowei Ye
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Huiyu Li
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Xiaoyang Liu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Iqbal Ahmad
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wenqiang Su
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Gongxun Zhong
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhiyuan Wen
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jinliang Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Rong-Hong Hua
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ao Ma
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Jie Liang
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Xiao-Peng Wan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Zhi-Gao Bu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Yong-Hui Zheng
- Department of Microbiology and Immunology, The University of Illinois Chicago, Chicago, IL, 60612, USA.
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Ahmad I, Fatemi SN, Ghaheri M, Rezvani A, Khezri DA, Natami M, Yasamineh S, Gholizadeh O, Bahmanyar Z. An overview of the role of Niemann-pick C1 (NPC1) in viral infections and inhibition of viral infections through NPC1 inhibitor. Cell Commun Signal 2023; 21:352. [PMID: 38098077 PMCID: PMC10722723 DOI: 10.1186/s12964-023-01376-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses communicate with their hosts through interactions with proteins, lipids, and carbohydrate moieties on the plasma membrane (PM), often resulting in viral absorption via receptor-mediated endocytosis. Many viruses cannot multiply unless the host's cholesterol level remains steady. The large endo/lysosomal membrane protein (MP) Niemann-Pick C1 (NPC1), which is involved in cellular cholesterol transport, is a crucial intracellular receptor for viral infection. NPC1 is a ubiquitous housekeeping protein essential for the controlled cholesterol efflux from lysosomes. Its human absence results in Niemann-Pick type C disease, a deadly lysosomal storage disorder. NPC1 is a crucial viral receptor and an essential host component for filovirus entrance, infection, and pathogenesis. For filovirus entrance, NPC1's cellular function is unnecessary. Furthermore, blocking NPC1 limits the entry and replication of the African swine fever virus by disrupting cholesterol homeostasis. Cell entrance of quasi-enveloped variants of hepatitis A virus and hepatitis E virus has also been linked to NPC1. By controlling cholesterol levels, NPC1 is also necessary for the effective release of reovirus cores into the cytoplasm. Drugs that limit NPC1's activity are effective against several viruses, including SARS-CoV and Type I Feline Coronavirus (F-CoV). These findings reveal NPC1 as a potential therapeutic target for treating viral illnesses and demonstrate its significance for several viral infections. This article provides a synopsis of NPC1's function in viral infections and a review of NPC1 inhibitors that may be used to counteract viral infections. Video Abstract.
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Affiliation(s)
- Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | | | - Mohammad Ghaheri
- Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran
| | - Ali Rezvani
- Anesthesiology Department, Case Western Reserve University, Cleveland, USA
| | - Dorsa Azizi Khezri
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Natami
- Department of Urology, Shahid Mohammadi Hospital, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | | | - Zahra Bahmanyar
- School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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3
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Matuozzo D, Talouarn E, Marchal A, Zhang P, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Abou Tayoun A, Aiuti A, Alavi Darazam I, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, Delmonte OM, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Metin Akcan O, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, de Diego RP, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Alosaimi MF, Alsohime FM, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. Genome Med 2023; 15:22. [PMID: 37020259 PMCID: PMC10074346 DOI: 10.1186/s13073-023-01173-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. METHODS We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. RESULTS No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P = 1.1 × 10-4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3-8.2], P = 2.1 × 10-4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1-2635.4], P = 3.4 × 10-3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3-8.4], P = 7.7 × 10-8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10-5). CONCLUSIONS Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.
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Affiliation(s)
- Daniela Matuozzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jeremy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | | | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Federica Barzaghi
- Department of Paediatric Immunohematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran, Iran
| | - Ahmad Abou Tayoun
- Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Ilad Alavi Darazam
- Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Infectious Diseases and Tropical Medicine, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Rebeca Alonso-Arias
- Immunology Department, Hospital Universitario Central de Asturias; Health Research Institute of Principality of Asturias, Oviedo, Spain
| | - Andrés Augusto Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Microbiology and Parasitology, Primary Immunodeficiencies Group, School of Medicine, University of Antioquia UdeA, 050010, Medellin, Colombia
- School of Microbiology, University of Antioquia UdeA, 050010, Medellin, Colombia
| | - Gokhan Aytekin
- Deparment of Internal Medicine, Division of Allergy and Immunology, Konya City Hospital, Konya, Turkey
| | - Peter Bergman
- Department of Infectious Diseases, The Immunodeficiency Unit, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Immunology, Stockholm, Sweden
| | - Simone Bondesan
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Yenan T Bryceson
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Oscar Cabrera-Marante
- Institute of Biomedical Research of IdiPAZ, University Hospital "La Paz", Madrid, Spain
| | - Sheila Carcel
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Paola Carrera
- Clinical Genomics, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Giorgio Casari
- Division of Genetics and Cell Biology, Genome-Phenome Relationship, San Raffaele Hospital, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Khalil Chaïbi
- Intensive Care Unit Department, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
- Common and Rare Kidney Diseases, Sorbonne University, INSERM UMR-S 1155, Paris, France
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Genetics Department, Immunology Division, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Laura E Covill
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Loubna El Zein
- Biology Department, Lebanese University, Beirut, Lebanon
| | - Carlos Flores
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Carlos III Health Institute, Madrid, Spain
- Research Unit, University Hospital of Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Peter K Gregersen
- Feinstein Institute for Medical Research, Northwell Health USA, Manhasset, NY, USA
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Filomeen Haerynck
- Department of Internal Diseases and Pediatrics, Primary Immune Deficiency Research Laboratory, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent, Belgium
| | - Rabih Halwani
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Selda Hancerli
- Department of Pediatrics (Infectious Diseases), Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Nevin Hatipoğlu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Adem Karbuz
- Department of Pediatric Infectious Disease, Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Sevgi Keles
- Meram Medical Faculty, Pediatric Infectious Diseases Department, Necmettin Erbakan University, Konya, Turkey
| | - Christèle Kyheng
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Rafael Leon-Lopez
- Unidad de Gestión Clínica de Cuidados Intensivos, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba (UCO), Córdoba, Spain
| | - Jose Luis Franco
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UDEA, Medellin, 050010, Colombia
| | - Davood Mansouri
- The Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Clinical Immunology and Infectious Diseases, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute and Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Institute for Health Science Research Germans Trias I Pujol (IGTP), Badalona, Spain
- Department of Infectious Diseases and Immunity, University of Vic-Central University of Catalonia, Vic, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ozge Metin Akcan
- Meram Medical Faculty, Pediatric Infectious Diseases Department, Necmettin Erbakan University, Konya, Turkey
| | - Isabelle Migeotte
- Centre de Génétique Humaine de L'Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille, France
- C2VN, INSERM, INRAE, Aix-Marseille University, Marseille, France
| | - Guillaume Morelle
- Department of General Paediatrics, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, University of Paris Saclay, Le Kremlin-Bicêtre, France
| | - Andrea Martin-Nalda
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Figen Palabiyik
- Pediatric Infectious Diseases Unit, Bakirkoy Dr Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | | | - Rebeca Pérez de Diego
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, University Hospital "La Paz", Madrid, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Daniel E Pleguezuelo
- Immunology Department, University Hospital 12 de Octubre, Research Institute imas12 and Complutense University, Madrid, Spain
| | - Carolina Prando
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Aurora Pujol
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | - Jacques G Rivière
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Carlos Rodriguez-Gallego
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrin, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Department of Clinical Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Julian Rojas
- Primary Immunodeficiencies Group, Department of Microbiology and Parasitology, School of Medicine, University of Antioquia UDEA, Medellin, 050010, Colombia
| | - Patrizia Rovere-Querini
- Vita-Salute San Raffaele University, Milan, Italy
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
- Center for Biomedical Research On Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Mohammad Shahrooei
- Specialized Immunology Laboratory of Dr Shahrooei, Sina Medical Complex, Ahvaz, Iran
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
| | - Ali Sobh
- Department of Pediatrics, Mansoura University Children's Hospital, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Pere Soler-Palacin
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona (UAB), Barcelona, Catalonia, Spain
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Yacine Tandjaoui-Lambiotte
- Hypoxia and Lung, INSERM U1272, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris, Bobigny, France
| | - Imran Tipu
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Cristina Tresoldi
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Jesus Troya
- Department of Internal Medicine, Infanta Leonor University Hospital, Madrid, Spain
| | - Diederik van de Beek
- Department of Neurology, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Mayana Zatz
- Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Pawel Zawadzki
- Gordion Bioscience Inc, Cambridge, MA, USA
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | - Saleh Zaid Al-Muhsen
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Faraj Alosaimi
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Fahad M Alsohime
- Department of Pediatrics, Immunology Research Laboratory, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hagit Baris-Feldman
- The Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manish J Butte
- Departments of Pediatrics and Microbiology, Immunology, and Molecular Genetics, Division of Immunology, Allergy, and Rheumatology, University of California Los Angeles, Los Angeles, CA, USA
| | - Stefan N Constantinescu
- Ludwig Institute for Cancer Research, Brussels, Belgium
- SIGN Unit, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Brussels, Belgium
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, Oxford University, Oxford, UK
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Richard P Lifton
- Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Tom Maniatis
- Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Horst von Bernuth
- Department of Paediatric Respiratory Medicine, Immunology, and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Alban Lermine
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Michel Vidaud
- Laboratoire de Biologie Médicale Multisites Seqoia, MG2025, MG2025, Paris, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | | | | | - France Mentre
- Unité de Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sarah Tubiana
- Centre d'Investigation Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d'immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Département de Santé Publique, Unité de Recherche Clinique PSL-CFX , CIC-1901, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France
- GRC-14 BIOFAST Sorbonn Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, NIAID, National Institutes of Health, Bethesda, MA, USA
| | - Stephanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.
- University Paris Cité, Imagine Institute, Paris, France.
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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4
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Assefi M, Bijan Rostami R, Ebrahimi M, Altafi M, Tehrany PM, Zaidan HK, Talib Al-Naqeeb BZ, Hadi M, Yasamineh S, Gholizadeh O. Potential use of the cholesterol transfer inhibitor U18666A as an antiviral drug for research on various viral infections. Microb Pathog 2023; 179:106096. [PMID: 37011734 DOI: 10.1016/j.micpath.2023.106096] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/04/2023]
Abstract
Cholesterol plays critical functions in arranging the biophysical attributes of proteins and lipids in the plasma membrane. For various viruses, an association with cholesterol for virus entrance and/or morphogenesis has been demonstrated. Therefore, the lipid metabolic pathways and the combination of membranes could be targeted to selectively suppress the virus replication steps as a basis for antiviral treatment. U18666A is a cationic amphiphilic drug (CAD) that affects intracellular transport and cholesterol production. A robust tool for investigating lysosomal cholesterol transfer and Ebola virus infection is an androstenolone derived termed U18666A that suppresses three enzymes in the cholesterol biosynthesis mechanism. In addition, U18666A inhibited low-density lipoprotein (LDL)-induced downregulation of LDL receptor and triggered lysosomal aggregation of cholesterol. According to reports, U18666A inhibits the reproduction of baculoviruses, filoviruses, hepatitis, coronaviruses, pseudorabies, HIV, influenza, and flaviviruses, as well as chikungunya and flaviviruses. U18666A-treated viral infections may act as a novel in vitro model system to elucidate the cholesterol mechanism of several viral infections. In this article, we discuss the mechanism and function of U18666A as a potent tool for studying cholesterol mechanisms in various viral infections.
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5
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Odongo L, Zadrozny KK, Diehl WE, Luban J, White JM, Ganser-Pornillos BK, Tamm LK, Pornillos O. Purification and structure of luminal domain C of human Niemann-Pick C1 protein. Acta Crystallogr F Struct Biol Commun 2023; 79:45-50. [PMID: 36748341 PMCID: PMC9903137 DOI: 10.1107/s2053230x23000705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Niemann-Pick C1 protein (NPC1) is a membrane protein that primarily resides in late endosomes and lysosomes, and plays an important role in cholesterol homeostasis in the cell. The second luminal domain of NPC1 (NPC1-C) serves as the intracellular receptor for Ebola and Marburg viruses. Here, the recombinant production of nonglycosylated and glycosylated NPC1-C and a new crystal form of the nonglycosylated protein are reported. The crystals belonged to space group P21 and diffracted to 2.3 Å resolution. The structure is similar to other reported structures of NPC1-C, with differences observed in the protruding loops when compared with NPC1-C in complex with Ebola virus glycoprotein or NPC2.
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Affiliation(s)
- Laura Odongo
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Kaneil K. Zadrozny
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - William E. Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Judith M. White
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Barbie K. Ganser-Pornillos
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Lukas K. Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA,Correspondence e-mail:
| | - Owen Pornillos
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
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6
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Matuozzo D, Talouarn E, Marchal A, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Zhang P, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Tayoun AA, Aiuti A, Darazam IA, Allende LM, Alonso-Arias R, Arias AA, Aytekin G, Bergman P, Bondesan S, Bryceson YT, Bustos IG, Cabrera-Marante O, Carcel S, Carrera P, Casari G, Chaïbi K, Colobran R, Condino-Neto A, Covill LE, El Zein L, Flores C, Gregersen PK, Gut M, Haerynck F, Halwani R, Hancerli S, Hammarström L, Hatipoğlu N, Karbuz A, Keles S, Kyheng C, Leon-Lopez R, Franco JL, Mansouri D, Martinez-Picado J, Akcan OM, Migeotte I, Morange PE, Morelle G, Martin-Nalda A, Novelli G, Novelli A, Ozcelik T, Palabiyik F, Pan-Hammarström Q, Pérez de Diego R, Planas-Serra L, Pleguezuelo DE, Prando C, Pujol A, Reyes LF, Rivière JG, Rodriguez-Gallego C, Rojas J, Rovere-Querini P, Schlüter A, Shahrooei M, Sobh A, Soler-Palacin P, Tandjaoui-Lambiotte Y, Tipu I, Tresoldi C, Troya J, van de Beek D, Zatz M, Zawadzki P, Al-Muhsen SZ, Baris-Feldman H, Butte MJ, Constantinescu SN, Cooper MA, Dalgard CL, Fellay J, Heath JR, Lau YL, Lifton RP, Maniatis T, Mogensen TH, von Bernuth H, Lermine A, Vidaud M, Boland A, Deleuze JF, Nussbaum R, Kahn-Kirby A, Mentre F, Tubiana S, Gorochov G, Tubach F, Hausfater P, Meyts I, Zhang SY, Puel A, Notarangelo LD, Boisson-Dupuis S, Su HC, Boisson B, Jouanguy E, Casanova JL, Zhang Q, Abel L, Cobat A. Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.10.22.22281221. [PMID: 36324795 PMCID: PMC9628204 DOI: 10.1101/2022.10.22.22281221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Background We previously reported inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity in 1-5% of unvaccinated patients with life-threatening COVID-19, and auto-antibodies against type I IFN in another 15-20% of cases. Methods We report here a genome-wide rare variant burden association analysis in 3,269 unvaccinated patients with life-threatening COVID-19 (1,301 previously reported and 1,968 new patients), and 1,373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. A quarter of the patients tested had antibodies against type I IFN (234 of 928) and were excluded from the analysis. Results No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7 , with an OR of 27.68 (95%CI:1.5-528.7, P= 1.1×10 -4 ), in analyses restricted to biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70 [95%CI:1.3-8.2], P= 2.1×10 -4 ). Adding the recently reported TYK2 COVID-19 locus strengthened this enrichment, particularly under a recessive model (OR=19.65 [95%CI:2.1-2635.4]; P= 3.4×10 -3 ). When these 14 loci and TLR7 were considered, all individuals hemizygous ( n =20) or homozygous ( n =5) for pLOF or bLOF variants were patients (OR=39.19 [95%CI:5.2-5037.0], P =4.7×10 -7 ), who also showed an enrichment in heterozygous variants (OR=2.36 [95%CI:1.0-5.9], P =0.02). Finally, the patients with pLOF or bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P= 1.68×10 -5 ). Conclusions Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.
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7
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Zhao J, Zhang H, Fan X, Yu X, Huai J. Lipid Dyshomeostasis and Inherited Cerebellar Ataxia. Mol Neurobiol 2022; 59:3800-3828. [PMID: 35420383 PMCID: PMC9148275 DOI: 10.1007/s12035-022-02826-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/01/2022] [Indexed: 12/04/2022]
Abstract
Cerebellar ataxia is a form of ataxia that originates from dysfunction of the cerebellum, but may involve additional neurological tissues. Its clinical symptoms are mainly characterized by the absence of voluntary muscle coordination and loss of control of movement with varying manifestations due to differences in severity, in the site of cerebellar damage and in the involvement of extracerebellar tissues. Cerebellar ataxia may be sporadic, acquired, and hereditary. Hereditary ataxia accounts for the majority of cases. Hereditary ataxia has been tentatively divided into several subtypes by scientists in the field, and nearly all of them remain incurable. This is mainly because the detailed mechanisms of these cerebellar disorders are incompletely understood. To precisely diagnose and treat these diseases, studies on their molecular mechanisms have been conducted extensively in the past. Accumulating evidence has demonstrated that some common pathogenic mechanisms exist within each subtype of inherited ataxia. However, no reports have indicated whether there is a common mechanism among the different subtypes of inherited cerebellar ataxia. In this review, we summarize the available references and databases on neurological disorders characterized by cerebellar ataxia and show that a subset of genes involved in lipid homeostasis form a new group that may cause ataxic disorders through a common mechanism. This common signaling pathway can provide a valuable reference for future diagnosis and treatment of ataxic disorders.
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Affiliation(s)
- Jin Zhao
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Huan Zhang
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Xueyu Fan
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Xue Yu
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China
| | - Jisen Huai
- The Second Affiliated Hospital of Xinxiang Medical University (Henan Mental Hospital), Xinxiang, 453000, China.
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, 453003, China.
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8
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Winkler MBL, Nel L, Frain KM, Dedic E, Olesen E, Pedersen BP. Sterol uptake by the NPC system in eukaryotes: a Saccharomyces cerevisiae perspective. FEBS Lett 2022; 596:160-179. [PMID: 34897668 DOI: 10.1002/1873-3468.14253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022]
Abstract
Sterols are an essential component of membranes in all eukaryotic cells and the precursor of multiple indispensable cellular metabolites. After endocytotic uptake, sterols are integrated into the lysosomal membrane by the Niemann-Pick type C (NPC) system before redistribution to other membranes. The process is driven by two proteins that, together, compose the NPC system: the lysosomal sterol shuttle protein NPC2 and the membrane protein NPC1 (named NCR1 in fungi), which integrates sterols into the lysosomal membrane. The Saccharomyces cerevisiae NPC system provides a compelling model to study the molecular mechanism of sterol integration into membranes and sterol homeostasis. This review summarizes recent advances in the field, and by interpreting available structural data, we propose a unifying conceptual model for sterol loading, transfer and transport by NPC proteins.
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Affiliation(s)
- Mikael B L Winkler
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Lynette Nel
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Kelly M Frain
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Emil Dedic
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Esben Olesen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
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9
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Shah S, Chougule MB, Kotha AK, Kashikar R, Godugu C, Raghuvanshi RS, Singh SB, Srivastava S. Nanomedicine based approaches for combating viral infections. J Control Release 2021; 338:80-104. [PMID: 34375690 PMCID: PMC8526416 DOI: 10.1016/j.jconrel.2021.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022]
Abstract
Millions of people die each year from viral infections across the globe. There is an urgent need to overcome the existing gap and pitfalls of the current antiviral therapy which include increased dose and dosing frequency, bioavailability challenges, non-specificity, incidences of resistance and so on. These stumbling blocks could be effectively managed by the advent of nanomedicine. Current review emphasizes over an enhanced understanding of how different lipid, polymer and elemental based nanoformulations could be potentially and precisely used to bridle the said drawbacks in antiviral therapy. The dawn of nanotechnology meeting vaccine delivery, role of RNAi therapeutics in antiviral treatment regimen, various regulatory concerns towards clinical translation of nanomedicine along with current trends and implications including unexplored research avenues for advancing the current drug delivery have been discussed in detail.
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Affiliation(s)
- Saurabh Shah
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Mahavir Bhupal Chougule
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, MS, USA; Department Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Arun K Kotha
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, MS, USA; Department Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Rama Kashikar
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, MS, USA; Department Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, USA
| | - Chandraiah Godugu
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Rajeev Singh Raghuvanshi
- Indian Pharmacopoeia Commission, Ministry of Health & Family Welfare, Government of India, India
| | - Shashi Bala Singh
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Saurabh Srivastava
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India.
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10
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Cross-Neutralisation of Novel Bombali Virus by Ebola Virus Antibodies and Convalescent Plasma Using an Optimised Pseudotype-Based Neutralisation Assay. Trop Med Infect Dis 2021; 6:tropicalmed6030155. [PMID: 34449756 PMCID: PMC8412100 DOI: 10.3390/tropicalmed6030155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 11/17/2022] Open
Abstract
Ebolaviruses continue to pose a significant outbreak threat, and while Ebola virus (EBOV)-specific vaccines and antivirals have been licensed, efforts to develop candidates offering broad species cross-protection are continuing. The use of pseudotyped virus in place of live virus is recognised as an alternative, safer, high-throughput platform to evaluate anti-ebolavirus antibodies towards their development, yet it requires optimisation. Here, we have shown that the target cell line impacts neutralisation assay results and cannot be selected purely based on permissiveness. In expanding the platform to incorporate each of the ebolavirus species envelope glycoprotein, allowing a comprehensive assessment of cross-neutralisation, we found that the recently discovered Bombali virus has a point mutation in the receptor-binding domain which prevents entry into a hamster cell line and, importantly, shows that this virus can be cross-neutralised by EBOV antibodies and convalescent plasma.
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11
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Potential pharmacological strategies targeting the Niemann-Pick C1 receptor and Ebola virus glycoprotein interaction. Eur J Med Chem 2021; 223:113654. [PMID: 34175537 DOI: 10.1016/j.ejmech.2021.113654] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/27/2021] [Accepted: 06/13/2021] [Indexed: 10/21/2022]
Abstract
Niemann-Pick C1 (NPC1) receptor is an intracellular protein located in late endosomes and lysosomes whose main function is to regulate intracellular cholesterol trafficking. Besides being postulated as necessary for the infection of highly pathogenic viruses in which the integrity of cholesterol transport is required, this protein also allows the entry of the Ebola virus (EBOV) into the host cells acting as an intracellular receptor. EBOV glycoprotein (EBOV-GP) interaction with NPC1 at the endosomal membrane triggers the release of the viral material into the host cell, starting the infective cycle. Disruption of the NPC1/EBOV-GP interaction could represent an attractive strategy for the development of drugs aimed at inhibiting viral entry and thus infection. Some of the today available EBOV inhibitors were proposed to interrupt this interaction, but molecular and structural details about their mode of action are still preliminary thus more efforts are needed to properly address these points. Here, we provide a critical discussion of the potential of NPC1 and its interaction with EBOV-GP as a therapeutic target for viral infections.
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12
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Baker S, Petukh M. Effect of pH on the Ability of N-Terminal Domain of Human NPC1 to Recognize, Bind, and Transfer Cholesterol. ACS OMEGA 2020; 5:29222-29230. [PMID: 33225153 PMCID: PMC7676335 DOI: 10.1021/acsomega.0c03983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Niemann-Pick type C1 (NPC1) is a large multidomain transmembrane protein essential for transporting cholesterol (CLR) from late endosomes and lysosomes to the endoplasmic reticulum and other cellular compartments. The lumen-facing N-terminal domain (NTD), involved in direct binding of CLR, is expected to have an optimum activity at acidic pH = 4.5. Here, we show that acidic pH is vital for the functionality of NPC1(NTD) and should be taken into account when studying the protein activity. We applied evolutionary, structural, and physicochemical analyses to decipher the consequences of a change in pH from acidic (pH = 4.5) to neutral (pH = 7.2) on the structural integrity of the NTD and its ability to bind CLR. We revealed that the change in pH from 4.5 to 7.2 increases the potential energy of the protein in both apo- and holo-states making the system less energetically favorable. At neutral pH, the flexibility of the protein in the apo-state is decreased caused by the alteration of specific interactions, which in turn might have a high impact on ligand recognition and binding. In contrast, neutral pH significantly exaggerates the flexibility of the protein with bound CLR that causes a partial exposure of the ligand to the water phase and its mislocation inside the ligand-binding pocket, which might obstruct CLR translocation through the membrane.
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13
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Gaisina IN, Peet NP, Wong L, Schafer AM, Cheng H, Anantpadma M, Davey RA, Thatcher GRJ, Rong L. Discovery and Structural Optimization of 4-(Aminomethyl)benzamides as Potent Entry Inhibitors of Ebola and Marburg Virus Infections. J Med Chem 2020; 63:7211-7225. [PMID: 32490678 DOI: 10.1021/acs.jmedchem.0c00463] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The recent Ebola epidemics in West Africa underscore the great need for effective and practical therapies for future Ebola virus outbreaks. We have discovered a new series of remarkably potent small molecule inhibitors of Ebola virus entry. These 4-(aminomethyl)benzamide-based inhibitors are also effective against Marburg virus. Synthetic routes to these compounds allowed for the preparation of a wide variety of structures, including a conformationally restrained subset of indolines (compounds 41-50). Compounds 20, 23, 32, 33, and 35 are superior inhibitors of Ebola (Mayinga) and Marburg (Angola) infectious viruses. Representative compounds (20, 32, and 35) have shown good metabolic stability in plasma and liver microsomes (rat and human), and 32 did not inhibit CYP3A4 nor CYP2C9. These 4-(aminomethyl)benzamides are suitable for further optimization as inhibitors of filovirus entry, with the potential to be developed as therapeutic agents for the treatment and control of Ebola virus infections.
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Affiliation(s)
- Irina N Gaisina
- UICentre (Drug Discovery @ UIC) and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States.,Chicago BioSolutions Inc., 2242 W Harrison Street, Chicago, Illinois 60612, United States
| | - Norton P Peet
- Chicago BioSolutions Inc., 2242 W Harrison Street, Chicago, Illinois 60612, United States
| | - Letitia Wong
- Chicago BioSolutions Inc., 2242 W Harrison Street, Chicago, Illinois 60612, United States
| | - Adam M Schafer
- College of Medicine, Department of Microbiology and Immunology, University of Illinois at Chicago, 909 S Wolcott Ave, Chicago, Illinois 60612, United States
| | - Han Cheng
- College of Medicine, Department of Microbiology and Immunology, University of Illinois at Chicago, 909 S Wolcott Ave, Chicago, Illinois 60612, United States
| | - Manu Anantpadma
- Texas Biomedical Research Institute, 8715 W Military Drive, San Antonio, Texas 78227, United States.,Department of Microbiology, Boston University, 620 Albany Street, Boston, Massachusetts 02118, United States
| | - Robert A Davey
- Texas Biomedical Research Institute, 8715 W Military Drive, San Antonio, Texas 78227, United States.,Department of Microbiology, Boston University, 620 Albany Street, Boston, Massachusetts 02118, United States
| | - Gregory R J Thatcher
- UICentre (Drug Discovery @ UIC) and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Lijun Rong
- College of Medicine, Department of Microbiology and Immunology, University of Illinois at Chicago, 909 S Wolcott Ave, Chicago, Illinois 60612, United States
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14
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Ouweneel AB, Thomas MJ, Sorci-Thomas MG. The ins and outs of lipid rafts: functions in intracellular cholesterol homeostasis, microparticles, and cell membranes: Thematic Review Series: Biology of Lipid Rafts. J Lipid Res 2020; 61:676-686. [PMID: 33715815 PMCID: PMC7193959 DOI: 10.1194/jlr.tr119000383] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Cellular membranes are not homogenous mixtures of proteins; rather, they are segregated into microdomains on the basis of preferential association between specific lipids and proteins. These microdomains, called lipid rafts, are well known for their role in receptor signaling on the plasma membrane (PM) and are essential to such cellular functions as signal transduction and spatial organization of the PM. A number of disease states, including atherosclerosis and other cardiovascular disorders, may be caused by dysfunctional maintenance of lipid rafts. Lipid rafts do not occur only in the PM but also have been found in intracellular membranes and extracellular vesicles (EVs). Here, we focus on discussing newly discovered functions of lipid rafts and microdomains in intracellular membranes, including lipid and protein trafficking from the ER, Golgi bodies, and endosomes to the PM, and we examine lipid raft involvement in the production and composition of EVs. Because lipid rafts are small and transient, visualization remains challenging. Future work with advanced techniques will continue to expand our knowledge about the roles of lipid rafts in cellular functioning.
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Affiliation(s)
- Amber B Ouweneel
- Department of Medicine, Division of Endocrinology and Molecular Medicine,Medical College of Wisconsin, Milwaukee, WI 53226; Cardiovascular Center,Medical College of Wisconsin, Milwaukee, WI 53226
| | - Michael J Thomas
- Cardiovascular Center,Medical College of Wisconsin, Milwaukee, WI 53226; Department of Pharmacology and Toxicology,Medical College of Wisconsin, Milwaukee, WI 53226
| | - Mary G Sorci-Thomas
- Department of Medicine, Division of Endocrinology and Molecular Medicine,Medical College of Wisconsin, Milwaukee, WI 53226; Cardiovascular Center,Medical College of Wisconsin, Milwaukee, WI 53226; Department of Pharmacology and Toxicology,Medical College of Wisconsin, Milwaukee, WI 53226. mailto:
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15
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Wang C, Scott SM, Subramanian K, Loguercio S, Zhao P, Hutt DM, Farhat NY, Porter FD, Balch WE. Quantitating the epigenetic transformation contributing to cholesterol homeostasis using Gaussian process. Nat Commun 2019; 10:5052. [PMID: 31699992 PMCID: PMC6838179 DOI: 10.1038/s41467-019-12969-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
To understand the impact of epigenetics on human misfolding disease, we apply Gaussian-process regression (GPR) based machine learning (ML) (GPR-ML) through variation spatial profiling (VSP). VSP generates population-based matrices describing the spatial covariance (SCV) relationships that link genetic diversity to fitness of the individual in response to histone deacetylases inhibitors (HDACi). Niemann-Pick C1 (NPC1) is a Mendelian disorder caused by >300 variants in the NPC1 gene that disrupt cholesterol homeostasis leading to the rapid onset and progression of neurodegenerative disease. We determine the sequence-to-function-to-structure relationships of the NPC1 polypeptide fold required for membrane trafficking and generation of a tunnel that mediates cholesterol flux in late endosomal/lysosomal (LE/Ly) compartments. HDACi treatment reveals unanticipated epigenomic plasticity in SCV relationships that restore NPC1 functionality. GPR-ML based matrices capture the epigenetic processes impacting information flow through central dogma, providing a framework for quantifying the effect of the environment on the healthspan of the individual.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - Samantha M Scott
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | | | - Salvatore Loguercio
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - Pei Zhao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - Nicole Y Farhat
- Section on Molecular Dysmorphology, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Forbes D Porter
- Section on Molecular Dysmorphology, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20814, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA.
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16
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McCauliff LA, Langan A, Li R, Ilnytska O, Bose D, Waghalter M, Lai K, Kahn PC, Storch J. Intracellular cholesterol trafficking is dependent upon NPC2 interaction with lysobisphosphatidic acid. eLife 2019; 8:50832. [PMID: 31580258 PMCID: PMC6855803 DOI: 10.7554/elife.50832] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 10/02/2019] [Indexed: 12/12/2022] Open
Abstract
Unesterified cholesterol accumulation in the late endosomal/lysosomal (LE/LY) compartment is the cellular hallmark of Niemann-Pick C (NPC) disease, caused by defects in the genes encoding NPC1 or NPC2. We previously reported the dramatic stimulation of NPC2 cholesterol transport rates to and from model membranes by the LE/LY phospholipid lysobisphosphatidic acid (LBPA). It had been previously shown that enrichment of NPC1-deficient cells with LBPA results in cholesterol clearance. Here we demonstrate that LBPA enrichment in human NPC2-deficient cells, either directly or via its biosynthetic precursor phosphtidylglycerol (PG), is entirely ineffective, indicating an obligate functional interaction between NPC2 and LBPA in cholesterol trafficking. We further demonstrate that NPC2 interacts directly with LBPA and identify the NPC2 hydrophobic knob domain as the site of interaction. Together these studies reveal a heretofore unknown step of intracellular cholesterol trafficking which is critically dependent upon the interaction of LBPA with functional NPC2 protein. Cholesterol is a type of fat that is essential for many processes in the body, such as repairing damaged cells and producing certain hormones. Normally, cholesterol enters cells from the bloodstream and is then moved to the parts of the cell that need it via a process known as ‘trafficking’. When cholesterol trafficking goes wrong, abnormally large amounts of cholesterol and other fats accumulate within the cell. Over time, these fatty deposits become toxic to cells and eventually damage the affected tissues. Niemann-Pick type C disease (NPC) is a severe genetic disorder affecting cholesterol trafficking. It is characterized by cholesterol build-up in multiple tissues, including the brain, which ultimately causes degeneration and death of nerve cells. Two proteins, NPC1 and NPC2, are involved in NPC disease. Both proteins normally help move cholesterol out of important trafficking compartments (known as the endosomal and lysosomal compartments) to other areas of the cell where it is needed. Patients with the disease can have mutations in either the gene for NPC1 or the gene for NPC2. This means that cells from NPC1 patients do not make enough functional NPC1 protein (but contain working NPC2), and vice versa. Previous studies had shown that giving cells with NPC1 mutations large amounts of the small molecule lysobisphosphatidic acid (LBPA for short) could compensate for the loss of NPC1, and stop the toxic build-up of cholesterol. McCauliff, Langan, Li et al. therefore wanted to explore exactly how LBPA was doing this. They had shown that LBPA dramatically increased the ability of purified NPC2 protein to transport cholesterol, and wondered if the effect of LBPA in the cells without NPC1 depended on NPC2. They predicted that boosting LBPA levels would not work in cells lacking NPC2. Biochemical experiments using purified protein showed that LBPA and NPC2 did indeed interact directly with each other. Systematically changing different building blocks of NPC2 revealed that a single region of the protein is sensitive to LBPA, and when this region was altered, LBPA could no longer interact with NPC2. Since LBPA is naturally produced by cells, they then stimulated cells grown in the laboratory to generate more LBPA using its precursor phosphatidylglycerol. They used cells from patients with mutations in either NPC1 or NPC2 and demonstrated that LBPA’s ability to reverse the accumulation of cholesterol was dependent on its interaction with NPC2. Thus, increasing LBPA levels in cells from patients with NPC1 mutations was beneficial, but had no effect on cells from patients with NPC2 mutations. These results shed new light not only on how cells transport cholesterol, but also on potential methods to combat disorders of cellular cholesterol trafficking. In the future, LBPA could be developed as a genetically tailored, patient-specific therapy for diseases like NPC.
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Affiliation(s)
- Leslie A McCauliff
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States.,Rutgers Center for Lipid Research, Rutgers University, New Brunswick, United States
| | - Annette Langan
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States.,Rutgers Center for Lipid Research, Rutgers University, New Brunswick, United States
| | - Ran Li
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States.,Rutgers Center for Lipid Research, Rutgers University, New Brunswick, United States
| | - Olga Ilnytska
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States.,Rutgers Center for Lipid Research, Rutgers University, New Brunswick, United States
| | - Debosreeta Bose
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States.,Rutgers Center for Lipid Research, Rutgers University, New Brunswick, United States
| | - Miriam Waghalter
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States
| | - Kimberly Lai
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States
| | - Peter C Kahn
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, United States
| | - Judith Storch
- Department of Nutritional Sciences, Rutgers University, New Brunswick, United States.,Rutgers Center for Lipid Research, Rutgers University, New Brunswick, United States
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17
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Pfeffer SR. NPC intracellular cholesterol transporter 1 (NPC1)-mediated cholesterol export from lysosomes. J Biol Chem 2019; 294:1706-1709. [PMID: 30710017 DOI: 10.1074/jbc.tm118.004165] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Low-density lipoprotein particles are taken up by cells and delivered to the lysosome where their cholesterol esters are cleaved off by acid lipase. The released, free cholesterol is then exported from lysosomes for cellular needs or storage. This article summarizes recent advances in our understanding of the molecular basis of cholesterol export from lysosomes. Cholesterol export requires NPC intracellular cholesterol transporter 1 (NPC1) and NPC2, genetic mutations of which can cause Niemann-Pick type C disease, a disorder characterized by massive lysosomal accumulation of cholesterol and glycosphingolipids. Analysis of the NPC1 and NPC2 structures and biochemical properties, together with new structures of the related Patched (PTCH) protein, provides new clues to the mechanisms by which NPC proteins may function.
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Affiliation(s)
- Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305-5307.
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18
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Shaikh F, Zhao Y, Alvarez L, Iliopoulou M, Lohans C, Schofield CJ, Padilla-Parra S, Siu SWI, Fry EE, Ren J, Stuart DI. Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library. J Med Chem 2019; 62:2928-2937. [PMID: 30785281 PMCID: PMC6441942 DOI: 10.1021/acs.jmedchem.8b01328] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
Potent Ebolavirus (EBOV) inhibitors
will help to curtail outbreaks
such as that which occurred in 2014–16 in West Africa. EBOV
has on its surface a single glycoprotein (GP) critical for viral entry
and membrane fusion. Recent high-resolution complexes of EBOV GP with
a variety of approved drugs revealed that binding to a common cavity
prevented fusion of the virus and endosomal membranes, inhibiting
virus infection. We performed docking experiments, screening a database
of natural compounds to identify those likely to bind at this site.
Using both inhibition assays of HIV-1-derived pseudovirus cell entry
and structural analyses of the complexes of the compounds with GP,
we show here that two of these compounds attach in the common binding
cavity, out of eight tested. In both cases, two molecules bind in
the cavity. The two compounds are chemically similar, but the tighter
binder has an additional chlorine atom that forms good halogen bonds
to the protein and achieves an IC50 of 50 nM, making it
the most potent GP-binding EBOV inhibitor yet identified, validating
our screening approach for the discovery of novel antiviral compounds.
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Affiliation(s)
- Faraz Shaikh
- Department of Computer and Information Science, Faculty of Science and Technology , University of Macau , E11, Macau 999078 , China.,Division of Structural Biology , University of Oxford , The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN , U.K
| | - Yuguang Zhao
- Division of Structural Biology , University of Oxford , The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN , U.K
| | - Luis Alvarez
- Division of Structural Biology , University of Oxford , The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN , U.K
| | - Maria Iliopoulou
- Division of Structural Biology , University of Oxford , The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN , U.K
| | - Christopher Lohans
- Department of Chemistry , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
| | | | - Sergi Padilla-Parra
- Division of Structural Biology , University of Oxford , The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN , U.K.,Biocruces-Bizkaia Health Research Institute , Ikerbasque, Basque Foundation for Science , Bilbao 48011 , Spain
| | - Shirley W I Siu
- Department of Computer and Information Science, Faculty of Science and Technology , University of Macau , E11, Macau 999078 , China
| | - Elizabeth E Fry
- Division of Structural Biology , University of Oxford , The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN , U.K
| | - Jingshan Ren
- Division of Structural Biology , University of Oxford , The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN , U.K
| | - David I Stuart
- Division of Structural Biology , University of Oxford , The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN , U.K.,Diamond Light Source Limited , Harwell Science & Innovation Campus , Didcot OX11 0DE , U.K
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19
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Petukh M, Zhulin IB. Comparative study of the effect of disease causing and benign mutations in position Q92 on cholesterol binding by the NPC1 n-terminal domain. Proteins 2018; 86:1165-1175. [PMID: 30183109 DOI: 10.1002/prot.25597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 11/06/2022]
Abstract
The Niemann-Pick type C1 (NPC1) protein is a large transmembrane protein located in lysosomes/endosomes. NPC1 binds cholesterol (CLR) and transports it to cellular membrane and endoplasmic reticulum. Mutations in NPC1 cause Niemann-Pick type C (NPC) disease, a rare autosomal disorder characterized by intracellular accumulations of CLR and subsequent neurodegeneration leading to premature death. Among known disease-causing mutations in NPC1, Q92R is the one that is located in the N-terminal cholesterol-binding domain [NTD]. Here we study the effect of the mutation on the ability of NPC1 (NTD) to bind and retain CLR in the binding pocket using structural analysis. We compare characteristics of the Q92R and Q92S mutant type (MT) protein, which is predicted to be benign. We provide detailed investigation of the CLR-NPC1 (NTD) binding process; and propose the mechanism, by which Q92R mutation causes NPC disease. We show that although Q92 residue neither directly participates in catalytic activity of the NPC1 (NTD), nor defines its CLR-binding specificity - it is important for the overall protein structure as well as for providing favorable electrostatic environment for CLR transfer. Our results suggest that a negative electrostatic potential of the CLR binding site (the S-opening) might promote NPC2 interaction with NPC1 (NTD) and/or proper CLR orientation and its enforced transfer. We show that in contrast to the benign Q92S mutation, Q92R significantly reduces electrostatic potential around S-opening, and thus likely affects NPC1 (NTD)-NPC2 interaction and/or CLR transfer from NPC2 to NPC1.
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Affiliation(s)
- Marharyta Petukh
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee.,Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Igor B Zhulin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee.,Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.,Center for Bioinformatics, Pavlov First Saint Petersburg State Medical University, Saint Petersburg, Russia
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20
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Mechanisms of cellular cholesterol compartmentalization: recent insights. Curr Opin Cell Biol 2018; 53:77-83. [PMID: 29960186 DOI: 10.1016/j.ceb.2018.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/07/2018] [Accepted: 06/05/2018] [Indexed: 11/20/2022]
Abstract
This review discusses advances in understanding how the controlled delivery of cholesterol between subcellular compartments is achieved and what novel experimental strategies are being employed to address this fundamental question. Recent work has focused on cholesterol-binding proteins that can facilitate directional cholesterol transfer between contacts of the ER and Golgi or late endosomal membranes. Increasing structural information on cholesterol-binding proteins, new modules engineered from them as well as improved imaging and gene editing techniques are providing valuable insights. There is also mounting information on how the crosstalk between cholesterol transport and nutrient signaling is orchestrated and how cellular fatty acid metabolism and cholesterol homeostasis are intertwined.
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21
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Wangeline MA, Vashistha N, Hampton RY. Proteostatic Tactics in the Strategy of Sterol Regulation. Annu Rev Cell Dev Biol 2018; 33:467-489. [PMID: 28992438 DOI: 10.1146/annurev-cellbio-111315-125036] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In eukaryotes, the synthesis and uptake of sterols undergo stringent multivalent regulation. Both individual enzymes and transcriptional networks are controlled to meet changing needs of the many sterol pathway products. Regulation is tailored by evolution to match regulatory constraints, which can be very different in distinct species. Nevertheless, a broadly conserved feature of many aspects of sterol regulation is employment of proteostasis mechanisms to bring about control of individual proteins. Proteostasis is the set of processes that maintain homeostasis of a dynamic proteome. Proteostasis includes protein quality control pathways for the detection, and then the correction or destruction, of the many misfolded proteins that arise as an unavoidable feature of protein-based life. Protein quality control displays not only the remarkable breadth needed to manage the wide variety of client molecules, but also extreme specificity toward the misfolded variants of a given protein. These features are amenable to evolutionary usurpation as a means to regulate proteins, and this approach has been used in sterol regulation. We describe both well-trod and less familiar versions of the interface between proteostasis and sterol regulation and suggest some underlying ideas with broad biological and clinical applicability.
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Affiliation(s)
- Margaret A Wangeline
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093;
| | - Nidhi Vashistha
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093;
| | - Randolph Y Hampton
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093;
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22
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Zhao Y, Ren J, Fry EE, Xiao J, Townsend AR, Stuart DI. Structures of Ebola Virus Glycoprotein Complexes with Tricyclic Antidepressant and Antipsychotic Drugs. J Med Chem 2018; 61:4938-4945. [DOI: 10.1021/acs.jmedchem.8b00350] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yuguang Zhao
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, U.K
| | - Jingshan Ren
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, U.K
| | - Elizabeth E. Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, U.K
| | - Julia Xiao
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, U.K
| | - Alain R. Townsend
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, U.K
| | - David I. Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, U.K
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, U.K
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23
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Lamri A, Pigeyre M, Garver WS, Meyre D. The Extending Spectrum of NPC1-Related Human Disorders: From Niemann-Pick C1 Disease to Obesity. Endocr Rev 2018; 39:192-220. [PMID: 29325023 PMCID: PMC5888214 DOI: 10.1210/er.2017-00176] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/02/2018] [Indexed: 12/22/2022]
Abstract
The Niemann-Pick type C1 (NPC1) protein regulates the transport of cholesterol and fatty acids from late endosomes/lysosomes and has a central role in maintaining lipid homeostasis. NPC1 loss-of-function mutations in humans cause NPC1 disease, a rare autosomal-recessive lipid-storage disorder characterized by progressive and lethal neurodegeneration, as well as liver and lung failure, due to cholesterol infiltration. In humans, genome-wide association studies and post-genome-wide association studies highlight the implication of common variants in NPC1 in adult-onset obesity, body fat mass, and type 2 diabetes. Heterozygous human carriers of rare loss-of-function coding variants in NPC1 display an increased risk of morbid adult obesity. These associations have been confirmed in mice models, showing an important interaction with high-fat diet. In this review, we describe the current state of knowledge for NPC1 variants in relationship to pleiotropic effects on metabolism. We provide evidence that NPC1 gene variations may predispose to common metabolic diseases by modulating steroid hormone synthesis and/or lipid homeostasis. We also propose several important directions of research to further define the complex roles of NPC1 in metabolism. This review emphasizes the contribution of NPC1 to obesity and its metabolic complications.
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Affiliation(s)
- Amel Lamri
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Marie Pigeyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada.,INSERM 1190, European Genomics Institute for Diabetes, University of Lille, CHRU Lille, Lille, France
| | - William S Garver
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico, Albuquerque, New Mexico
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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24
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Gale P. Using thermodynamic parameters to calibrate a mechanistic dose-response for infection of a host by a virus. MICROBIAL RISK ANALYSIS 2018; 8:1-13. [PMID: 32289059 PMCID: PMC7103988 DOI: 10.1016/j.mran.2018.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/29/2017] [Accepted: 01/03/2018] [Indexed: 05/21/2023]
Abstract
Assessing the risk of infection from emerging viruses or of existing viruses jumping the species barrier into novel hosts is limited by the lack of dose response data. The initial stages of the infection of a host by a virus involve a series of specific contact interactions between molecules in the host and on the virus surface. The strength of the interaction is quantified in the literature by the dissociation constant (Kd) which is determined experimentally and is specific for a given virus molecule/host molecule combination. Here, two stages of the initial infection process of host intestinal cells are modelled, namely escape of the virus in the oral challenge dose from the innate host defenses (e.g. mucin proteins in mucus) and the subsequent binding of any surviving virus to receptor molecules on the surface of the host epithelial cells. The strength of virus binding to host cells and to mucins may be quantified by the association constants, Ka and Kmucin, respectively. Here, a mechanistic dose-response model for the probability of infection of a host by a given virus dose is constructed using Ka and Kmucin which may be derived from published Kd values taking into account the number of specific molecular interactions. It is shown that the effectiveness of the mucus barrier is determined not only by the amount of mucin but also by the magnitude of Kmucin. At very high Kmucin values, slight excesses of mucin over virus are sufficient to remove all the virus according to the model. At lower Kmucin values, high numbers of virus may escape even with large excesses of mucin. The output from the mechanistic model is the probability (p1) of infection by a single virion which is the parameter used in conventional dose-response models to predict the risk of infection of the host from the ingested dose. It is shown here how differences in Ka (due to molecular differences in an emerging virus strain or new host) affect p1, and how these differences in Ka may be quantified in terms of two thermodynamic parameters, namely enthalpy and entropy. This provides the theoretical link between sequencing data and risk of infection. Lack of data on entropy is a limitation at present and may also affect our interpretation of Kd in terms of infectivity. It is concluded that thermodynamic approaches have a major contribution to make in developing dose-response models for emerging viruses.
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Key Words
- Asp, aspartate
- CRD, carbohydrate-recognition domain
- Cr, host cell receptor
- Dose-response
- EBOV, Zaire ebolavirus
- Enthalpy
- Entropy
- G, Gibbs free energy
- GI, gastrointestinal
- GP, glycoprotein
- H, enthalpy
- HA, haemagglutinin
- HBGA, histoblood group antigen
- HeV, Hendra virus
- Ka, Kmucin, association constants
- Kd, dissociation constant for two molecules bound to each other
- L, Avogadro number
- M, molar (moles dm−3)
- MBP, mannose binding protein
- MERS-CoV, MERS coronavirus
- MRA, microbiological risk assessment
- Mucin
- NPC1, Niemann-Pick C1 protein
- NiV, Nipah virus
- NoV, norovirus
- PL, phospholipid
- PRR, pathogen recognition receptor
- Phe, phenylalanine
- R, ideal gas constant
- S, entropy
- SPR, surface plasmon resonance
- T, temperature
- TIM-1, T-cell immunoglobulin and mucin domain protein 1
- VSV, vesicular stomatitis virus
- Virus
- k, on/off rate constant
- n, number of GP/Cr molecular contacts per virus/host cell binding
- pfu, plaque-forming unit
- ΔGa, change in Gibbs free energy on association of virus and cell
- ΔHa, change in enthalpy on association of virus and cell
- ΔSa, change in entropy on association of virus and cell
- ΔΔHa, change in ΔHa
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25
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Benussi A, Cotelli MS, Padovani A, Borroni B. Recent neuroimaging, neurophysiological, and neuropathological advances for the understanding of NPC. F1000Res 2018; 7:194. [PMID: 29511534 PMCID: PMC5814740 DOI: 10.12688/f1000research.12361.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/13/2018] [Indexed: 12/20/2022] Open
Abstract
Niemann–Pick disease type C (NPC) is a rare autosomal recessive lysosomal storage disorder with extensive biological, molecular, and clinical heterogeneity. Recently, numerous studies have tried to shed light on the pathophysiology of the disease, highlighting possible disease pathways common to other neurodegenerative disorders, such as Alzheimer’s disease and frontotemporal dementia, and identifying possible candidate biomarkers for disease staging and response to treatment. Miglustat, which reversibly inhibits glycosphingolipid synthesis, has been licensed in the European Union and elsewhere for the treatment of NPC in both children and adults. A number of ongoing clinical trials might hold promise for the development of new treatments for NPC. The objective of the present work is to review and evaluate recent literature data in order to highlight the latest neuroimaging, neurophysiological, and neuropathological advances for the understanding of NPC pathophysiology. Furthermore, ongoing developments in disease-modifying treatments will be briefly discussed.
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Affiliation(s)
- Alberto Benussi
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa, 11, 25123 Brescia BS, Italy
| | | | - Alessandro Padovani
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa, 11, 25123 Brescia BS, Italy
| | - Barbara Borroni
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa, 11, 25123 Brescia BS, Italy
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Ren J, Zhao Y, Fry EE, Stuart DI. Target Identification and Mode of Action of Four Chemically Divergent Drugs against Ebolavirus Infection. J Med Chem 2018; 61:724-733. [PMID: 29272110 PMCID: PMC5808380 DOI: 10.1021/acs.jmedchem.7b01249] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here, we show that four chemically divergent approved drugs reported to inhibit Ebolavirus infection, benztropine, bepridil, paroxetine and sertraline, directly interact with the Ebolavirus glycoprotein. Binding of these drugs destabilizes the protein, suggesting that this may be the mechanism of inhibition, as reported for the anticancer drug toremifene and the painkiller ibuprofen, which bind in the same large cavity on the glycoprotein. Crystal structures show that the position of binding and the mode of interaction within the pocket vary significantly between these compounds. The binding constants (Kd) determined by thermal shift assay correlate with the protein-inhibitor interactions as well as with the antiviral activities determined by virus cell entry assays, supporting the hypothesis that these drugs inhibit viral entry by binding the glycoprotein and destabilizing the prefusion conformation. Details of the protein-inhibitor interactions of these complexes and their relation with binding affinity may facilitate the design of more potent inhibitors.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, University of Oxford , The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, U.K
| | - Yuguang Zhao
- Division of Structural Biology, University of Oxford , The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, U.K
| | - Elizabeth E Fry
- Division of Structural Biology, University of Oxford , The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, U.K
| | - David I Stuart
- Division of Structural Biology, University of Oxford , The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, U.K.,Diamond Light Source Ltd. , Harwell Science & Innovation Campus, Didcot, OX11 0DE, U.K
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27
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King LB, Fusco ML, Flyak AI, Ilinykh PA, Huang K, Gunn B, Kirchdoerfer RN, Hastie KM, Sangha AK, Meiler J, Alter G, Bukreyev A, Crowe JE, Saphire EO. The Marburgvirus-Neutralizing Human Monoclonal Antibody MR191 Targets a Conserved Site to Block Virus Receptor Binding. Cell Host Microbe 2018; 23:101-109.e4. [PMID: 29324225 PMCID: PMC5772738 DOI: 10.1016/j.chom.2017.12.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/28/2017] [Accepted: 12/08/2017] [Indexed: 11/22/2022]
Abstract
Since their first identification 50 years ago, marburgviruses have emerged several times, with 83%-90% lethality in the largest outbreaks. Although no vaccines or therapeutics are available for human use, the human antibody MR191 provides complete protection in non-human primates when delivered several days after inoculation of a lethal marburgvirus dose. The detailed neutralization mechanism of MR191 remains outstanding. Here we present a 3.2 Å crystal structure of MR191 complexed with a trimeric marburgvirus surface glycoprotein (GP). MR191 neutralizes by occupying the conserved receptor-binding site and competing with the host receptor Niemann-Pick C1. The structure illuminates previously disordered regions of GP including the stalk, fusion loop, CX6CC switch, and an N-terminal region of GP2 that wraps about the outside of GP1 to anchor a marburgvirus-specific "wing" antibody epitope. Virus escape mutations mapped far outside the MR191 receptor-binding site footprint suggest a role for these other regions in the GP quaternary structure.
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Affiliation(s)
- Liam B King
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marnie L Fusco
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew I Flyak
- Departments of Pediatrics, Pathology, Microbiology, and Immunology, and the Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Philipp A Ilinykh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Galveston National Laboratory, Galveston, TX 77550, USA
| | - Kai Huang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Galveston National Laboratory, Galveston, TX 77550, USA
| | - Bronwyn Gunn
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Robert N Kirchdoerfer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kathryn M Hastie
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amandeep K Sangha
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Galveston National Laboratory, Galveston, TX 77550, USA
| | - James E Crowe
- Departments of Pediatrics, Pathology, Microbiology, and Immunology, and the Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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28
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Enkavi G, Mikkolainen H, Güngör B, Ikonen E, Vattulainen I. Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin. PLoS Comput Biol 2017; 13:e1005831. [PMID: 29084218 PMCID: PMC5679659 DOI: 10.1371/journal.pcbi.1005831] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/09/2017] [Accepted: 10/19/2017] [Indexed: 11/19/2022] Open
Abstract
Niemann-Pick Protein C2 (npc2) is a small soluble protein critical for cholesterol transport within and from the lysosome and the late endosome. Intriguingly, npc2-mediated cholesterol transport has been shown to be modulated by lipids, yet the molecular mechanism of npc2-membrane interactions has remained elusive. Here, based on an extensive set of atomistic simulations and free energy calculations, we clarify the mechanism and energetics of npc2-membrane binding and characterize the roles of physiologically relevant key lipids associated with the binding process. Our results capture in atomistic detail two competitively favorable membrane binding orientations of npc2 with a low interconversion barrier. The first binding mode (Prone) places the cholesterol binding pocket in direct contact with the membrane and is characterized by membrane insertion of a loop (V59-M60-G61-I62-P63-V64-P65). This mode is associated with cholesterol uptake and release. On the other hand, the second mode (Supine) places the cholesterol binding pocket away from the membrane surface, but has overall higher membrane binding affinity. We determined that bis(monoacylglycero)phosphate (bmp) is specifically required for strong membrane binding in Prone mode, and that it cannot be substituted by other anionic lipids. Meanwhile, sphingomyelin counteracts bmp by hindering Prone mode without affecting Supine mode. Our results provide concrete evidence that lipids modulate npc2-mediated cholesterol transport either by favoring or disfavoring Prone mode and that they impose this by modulating the accessibility of bmp for interacting with npc2. Overall, we provide a mechanism by which npc2-mediated cholesterol transport is controlled by the membrane composition and how npc2-lipid interactions can regulate the transport rate.
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Affiliation(s)
- Giray Enkavi
- Laboratory of Physics, Tampere University of Technology, Tampere, Finland
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Heikki Mikkolainen
- Laboratory of Physics, Tampere University of Technology, Tampere, Finland
| | - Burçin Güngör
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Elina Ikonen
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology, Tampere, Finland
- Department of Physics, University of Helsinki, Helsinki, Finland
- Memphys—Center for Biomembrane Physics, Odense, Denmark
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29
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3.3 Å structure of Niemann-Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport. Proc Natl Acad Sci U S A 2017; 114:9116-9121. [PMID: 28784760 DOI: 10.1073/pnas.1711716114] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Niemann-Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann-Pick type C disease, a lysosomal storage disease. Despite recent reports of the NPC1 structure depicting its overall architecture, the function of its C-terminal luminal domain (CTD) remains poorly understood even though 45% of NPC disease-causing mutations are in this domain. Here, we report a crystal structure at 3.3 Å resolution of NPC1* (residues 314-1,278), which-in contrast to previous lower resolution structures-features the entire CTD well resolved. Notably, all eight cysteines of the CTD form four disulfide bonds, one of which (C909-C914) enforces a specific loop that in turn mediates an interaction with a loop of the N-terminal domain (NTD). Importantly, this loop and its interaction with the NTD were not observed in any previous structures due to the lower resolution. Our mutagenesis experiments highlight the physiological relevance of the CTD-NTD interaction, which might function to keep the NTD in the proper orientation for receiving cholesterol from NPC2. Additionally, this structure allows us to more precisely map all of the disease-causing mutations, allowing future molecular insights into the pathogenesis of NPC disease.
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30
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Structure of the Ebola virus glycoprotein spike within the virion envelope at 11 Å resolution. Sci Rep 2017; 7:46374. [PMID: 28397863 PMCID: PMC5387728 DOI: 10.1038/srep46374] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/15/2017] [Indexed: 12/29/2022] Open
Abstract
We present the structure of the surface Ebola virus (EBOV) trimeric glycoprotein (GP) spike at 11 Å resolution, in situ within the viral plasma membrane of purified virus particles. GP functions in cellular attachment, endosomal entry, and membrane fusion to initiate infection, and is a key therapeutic target. Nevertheless, only about half of the GP molecule has yet been solved to atomic resolution, excluding the mucin-like and transmembrane domains, and some of the glycans. Fitting of the atomic resolution X-ray data from expressed, truncated deletion constructs within our 11 Å structure of the entire molecule demonstrates the relationship between the GP1-GP2 domains, the mucin-like and transmembrane domains, and the bilaminar lipid envelope. We show that the mucin-like domain covers the glycan cap and partially occludes the receptor binding sites prior to proteolytic cleavage. Our structure is also consistent with key antibody neutralisation sites on GP being accessible prior to proteolysis. Based on the findings of us and others, GP-mediated binding may create an angle of 18 degrees between the planes of viral and endosomal membranes.
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31
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Diehl WE, Lin AE, Grubaugh ND, Carvalho LM, Kim K, Kyawe PP, McCauley SM, Donnard E, Kucukural A, McDonel P, Schaffner SF, Garber M, Rambaut A, Andersen KG, Sabeti PC, Luban J. Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic. Cell 2016; 167:1088-1098.e6. [PMID: 27814506 PMCID: PMC5115602 DOI: 10.1016/j.cell.2016.10.014] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/23/2016] [Accepted: 10/06/2016] [Indexed: 11/18/2022]
Abstract
The magnitude of the 2013-2016 Ebola virus disease (EVD) epidemic enabled an unprecedented number of viral mutations to occur over successive human-to-human transmission events, increasing the probability that adaptation to the human host occurred during the outbreak. We investigated one nonsynonymous mutation, Ebola virus (EBOV) glycoprotein (GP) mutant A82V, for its effect on viral infectivity. This mutation, located at the NPC1-binding site on EBOV GP, occurred early in the 2013-2016 outbreak and rose to high frequency. We found that GP-A82V had heightened ability to infect primate cells, including human dendritic cells. The increased infectivity was restricted to cells that have primate-specific NPC1 sequences at the EBOV interface, suggesting that this mutation was indeed an adaptation to the human host. GP-A82V was associated with increased mortality, consistent with the hypothesis that the heightened intrinsic infectivity of GP-A82V contributed to disease severity during the EVD epidemic.
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Affiliation(s)
- William E Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Luiz Max Carvalho
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, Scotland, UK
| | - Kyusik Kim
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Pyae Phyo Kyawe
- Department of Medicine, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01605, USA
| | - Sean M McCauley
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Elisa Donnard
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Alper Kucukural
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Patrick McDonel
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Manuel Garber
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, Scotland, UK
| | - Kristian G Andersen
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Scripps Translational Science Institute, 3344 North Torrey Pines Court, La Jolla, CA 92037, USA.
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
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32
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Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry. Antiviral Res 2016; 135:1-14. [PMID: 27640102 PMCID: PMC7113884 DOI: 10.1016/j.antiviral.2016.09.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/01/2016] [Accepted: 09/05/2016] [Indexed: 12/20/2022]
Abstract
This review focuses on the recent progress in our understanding of filovirus protein structure/function and its impact on antiviral research. Here we focus on the surface glycoprotein GP1,2 and its different roles in filovirus entry. We first describe the latest advances on the characterization of GP gene-overlapping proteins sGP, ssGP and Δ-peptide. Then, we compare filovirus surface GP1,2 proteins in terms of structure, synthesis and function. As they bear potential in drug-design, the discovery of small organic compounds inhibiting filovirus entry is a currently very active field. Although it is at an early stage, the development of antiviral drugs against Ebola and Marburg virus entry might prove essential to reduce outbreak-associated fatality rates through post-exposure treatment of both suspected and confirmed cases. The filovirus surface glycoprotein is the key player protein responsible for viral entry. Secreted forms of the glycoprotein have been suggested to participate to filovirus virus pathogenicity. Recent structural insights of the filovirus surface glycoprotein highlight new antiviral perspectives. Interesting compounds and innovative antiviral strategies emerge from research and development to inhibit filovirus entry.
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33
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Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2. Proc Natl Acad Sci U S A 2016; 113:10079-84. [PMID: 27551080 DOI: 10.1073/pnas.1611956113] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Export of LDL-derived cholesterol from lysosomes requires the cooperation of the integral membrane protein Niemann-Pick C1 (NPC1) and a soluble protein, Niemann-Pick C2 (NPC2). Mutations in the genes encoding these proteins lead to Niemann-Pick disease type C (NPC). NPC2 binds to NPC1's second (middle), lumenally oriented domain (MLD) and transfers cholesterol to NPC1's N-terminal domain (NTD). Here, we report the 2.4-Å resolution crystal structure of a complex of human NPC1-MLD and NPC2 bearing bound cholesterol-3-O-sulfate. NPC1-MLD uses two protruding loops to bind NPC2, analogous to its interaction with the primed Ebola virus glycoprotein. Docking of the NPC1-NPC2 complex onto the full-length NPC1 structure reveals a direct cholesterol transfer tunnel between NPC2 and NTD cholesterol binding pockets, supporting the "hydrophobic hand-off" cholesterol transfer model.
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35
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Toremifene interacts with and destabilizes the Ebola virus glycoprotein. Nature 2016; 535:169-172. [PMID: 27362232 PMCID: PMC4947387 DOI: 10.1038/nature18615] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/26/2016] [Indexed: 12/17/2022]
Abstract
Ebola viruses (EBOVs) are responsible for repeated outbreaks of fatal infections, including the recent deadly epidemic in West Africa. There are currently no approved therapeutic drugs or vaccines for the disease. EBOV has a membrane envelope decorated by trimers of a glycoprotein (GP, cleaved by furin to form GP1 and GP2 subunits) which is solely responsible for host cell attachment, endosomal entry and membrane fusion1–7. GP is thus a primary target for the development of antiviral drugs. Here we report the first unliganded structure of EBOV GP, and complexes with an anticancer drug toremifene and the painkiller ibuprofen. The high-resolution apo structure gives a more complete and accurate picture of the molecule, and allows conformational changes introduced by antibody and receptor binding to be deciphered8–10. Unexpectedly both toremifene and ibuprofen bind in a cavity between the attachment (GP1) and fusion (GP2) subunits at the entrance to a large tunnel that links with equivalent tunnels from the other monomers of the trimer at the 3-fold axis. Protein-drug interactions, with both GP1 and GP2, are predominately hydrophobic. Residues lining the binding site are highly conserved amongst filoviruses except Marburg virus (MARV), suggesting that MARV may not bind these drugs. Thermal shift assays show up to a 14 °C decrease in protein melting temperature upon toremifene binding, while ibuprofen has only a marginal effect and is a less potent inhibitor. The results suggest that inhibitor binding destabilizes GP and triggers premature release of GP2, therefore preventing fusion between the viral and endosome membranes. Thus these complex structures reveal the mechanism of inhibition and may guide the development of more powerful anti-EBOV drugs.
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Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection. Cell 2016; 165:1467-1478. [PMID: 27238017 PMCID: PMC7111323 DOI: 10.1016/j.cell.2016.05.022] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/22/2016] [Accepted: 05/03/2016] [Indexed: 11/22/2022]
Abstract
Niemann-Pick disease type C (NPC) is associated with mutations in NPC1 and NPC2, whose gene products are key players in the endosomal/lysosomal egress of low-density lipoprotein-derived cholesterol. NPC1 is also the intracellular receptor for Ebola virus (EBOV). Here, we present a 4.4 Å structure of full-length human NPC1 and a low-resolution reconstruction of NPC1 in complex with the cleaved glycoprotein (GPcl) of EBOV, both determined by single-particle electron cryomicroscopy. NPC1 contains 13 transmembrane segments (TMs) and three distinct lumenal domains A (also designated NTD), C, and I. TMs 2–13 exhibit a typical resistance-nodulation-cell division fold, among which TMs 3–7 constitute the sterol-sensing domain conserved in several proteins involved in cholesterol metabolism and signaling. A trimeric EBOV-GPcl binds to one NPC1 monomer through the domain C. Our structural and biochemical characterizations provide an important framework for mechanistic understanding of NPC1-mediated intracellular cholesterol trafficking and Ebola virus infection. The cryo-EM structure of full-length human NPC1 was determined at 4.4 Å resolution Structure-guided biochemical analysis of cholesterol transfer from NPC2 to NPC1 Low-resolution cryo-EM structure of NPC1 bound to GPcl of Ebola virus was obtained A trimeric GPcl binds to one NPC1 through the crystal structure-revealed interface
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